diff options
Diffstat (limited to 'wqflask/tests')
| -rw-r--r-- | wqflask/tests/unit/wqflask/api/test_gen_menu.py | 408 |
1 files changed, 216 insertions, 192 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py index fd0fe52e..743b3bde 100644 --- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py +++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py @@ -2,7 +2,6 @@ import unittest from unittest import mock -from wqflask import app from wqflask.api.gen_menu import gen_dropdown_json from wqflask.api.gen_menu import get_species from wqflask.api.gen_menu import get_groups @@ -18,8 +17,6 @@ class TestGenMenu(unittest.TestCase): """Tests for the gen_menu module""" def setUp(self): - self.app_context = app.app_context() - self.app_context.push() self.test_group = { 'mouse': [ ['H_T1', @@ -70,212 +67,239 @@ class TestGenMenu(unittest.TestCase): } } - def tearDown(self): - self.app_context.pop() - - @mock.patch('wqflask.api.gen_menu.g') - def test_get_species(self, db_mock): + def test_get_species(self): """Test that assertion is raised when dataset and dataset_name are defined""" - db_mock.db.execute.return_value.fetchall.return_value = ( - ('human', 'Human'), - ('mouse', 'Mouse')) - self.assertEqual(get_species(), - [['human', 'Human'], ['mouse', 'Mouse']]) - db_mock.db.execute.assert_called_once_with( - "SELECT Name, MenuName FROM Species ORDER BY OrderId" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_get_groups(self, db_mock): - """Test that species groups are grouped correctly""" - db_mock.db.execute.return_value.fetchall.side_effect = [ - # Mouse - (('BXD', 'BXD', None), - ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', - 'Test')), - # Human - (('H_T1', "H_T", "DescriptionA"), - ('H_T2', "H_T'", None)) - ] - - self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]), - self.test_group) - - for name in ["mouse", "human"]: - db_mock.db.execute.assert_any_call( - ("SELECT InbredSet.Name, InbredSet.FullName, " + - "IFNULL(InbredSet.Family, 'None') " - + "FROM InbredSet, Species WHERE Species.Name " - + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " - + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " - + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " - + "InbredSet.FullName) ASC, InbredSet.FullName ASC, " - + "InbredSet.MenuOrderId ASC").format(name) + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + ('human', 'Human'), + ('mouse', 'Mouse')) + self.assertEqual(get_species(db_mock), + [['human', 'Human'], ['mouse', 'Mouse']]) + cursor.execute.assert_called_once_with( + "SELECT Name, MenuName FROM Species ORDER BY OrderId" ) - @mock.patch('wqflask.api.gen_menu.g') - def test_phenotypes_exist_called_with_correct_query(self, db_mock): + def test_get_groups(self): + """Test that species groups are grouped correctly""" + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.side_effect = [ + # Mouse + (('BXD', 'BXD', None), + ('HLC', ('Liver: Normal Gene Expression ' + 'with Genotypes (Merck)'), + 'Test')), + # Human + (('H_T1', "H_T", "DescriptionA"), + ('H_T2', "H_T'", None)) + ] + self.assertEqual(get_groups([["human", "Human"], + ["mouse", "Mouse"]], + db_mock), + self.test_group) + + for name in ["mouse", "human"]: + cursor.execute.assert_any_call( + ("SELECT InbredSet.Name, InbredSet.FullName, " + "IFNULL(InbredSet.Family, 'None') " + "FROM InbredSet, Species WHERE Species.Name " + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " + "InbredSet.FullName) ASC, InbredSet.FullName ASC, " + "InbredSet.MenuOrderId ASC").format(name) + ) + + def test_phenotypes_exist_called_with_correct_query(self): """Test that phenotypes_exist is called with the correct query""" - db_mock.db.execute.return_value.fetchone.return_value = None - phenotypes_exist("test") - db_mock.db.execute.assert_called_with( - "SELECT Name FROM PublishFreeze " - "WHERE PublishFreeze.Name = 'testPublish'" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_phenotypes_exist_with_falsy_values(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = None + phenotypes_exist("test", db_mock) + cursor.execute.assert_called_with( + "SELECT Name FROM PublishFreeze " + "WHERE PublishFreeze.Name = 'testPublish'" + ) + + def test_phenotypes_exist_with_falsy_values(self): """Test that phenotype check returns correctly when given a None value""" - for x in [None, False, (), [], ""]: - db_mock.db.execute.return_value.fetchone.return_value = x - self.assertFalse(phenotypes_exist("test")) - - @mock.patch('wqflask.api.gen_menu.g') - def test_phenotypes_exist_with_truthy_value(self, db_mock): - """Test that phenotype check returns correctly when given Truthy """ - for x in ["x", ("result"), ["result"], [1]]: - db_mock.db.execute.return_value.fetchone.return_value = (x) - self.assertTrue(phenotypes_exist("test")) - - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_called_with_correct_query(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + for x in [None, False, (), [], ""]: + cursor.fetchone.return_value = x + self.assertFalse(phenotypes_exist("test", db_mock)) + + def test_phenotypes_exist_with_truthy_value(self): + """Test that phenotype check returns correctly when given Truthy""" + db_mock = mock.MagicMock() + with db_mock.cursor() as conn: + with conn.cursor() as cursor: + for x in ["x", ("result"), ["result"], [1]]: + cursor.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test", db_mock)) + + def test_genotypes_exist_called_with_correct_query(self): """Test that genotypes_exist is called with the correct query""" - db_mock.db.execute.return_value.fetchone.return_value = None - genotypes_exist("test") - db_mock.db.execute.assert_called_with( - "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_with_falsy_values(self, db_mock): - """Test that genotype check returns correctly when given - a None value""" - for x in [None, False, (), [], ""]: - db_mock.db.execute.return_value.fetchone.return_value = x - self.assertFalse(genotypes_exist("test")) + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = None + genotypes_exist("test", db_mock) + cursor.execute.assert_called_with( + "SELECT Name FROM GenoFreeze WHERE " + "GenoFreeze.Name = 'testGeno'" + ) + + def test_genotypes_exist_with_falsy_values(self): + """Test that genotype check returns correctly when given a None value + + """ + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + for x in [None, False, (), [], ""]: + cursor.fetchone.return_value = x + self.assertFalse(genotypes_exist("test", db_mock)) - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_with_truthy_value(self, db_mock): + def test_genotypes_exist_with_truthy_value(self): """Test that genotype check returns correctly when given Truthy """ - for x in ["x", ("result"), ["result"], [1]]: - db_mock.db.execute.return_value.fetchone.return_value = (x) - self.assertTrue(phenotypes_exist("test")) + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + for x in ["x", ("result"), ["result"], [1]]: + cursor.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test", db_mock)) - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_phenotypes(self, db_mock): + def test_build_datasets_with_type_phenotypes(self): """Test that correct dataset is returned for a phenotype type""" - db_mock.db.execute.return_value.fetchall.return_value = ( - (602, "BXDPublish", "BXD Published Phenotypes"), - ) - self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), - [['602', "BXDPublish", "BXD Published Phenotypes"]]) - db_mock.db.execute.assert_called_with( - "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " - + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " - + "InbredSet WHERE InbredSet.Name = 'BXD' AND " - + "PublishFreeze.InbredSetId = InbredSet.Id AND " - + "InfoFiles.InfoPageName = PublishFreeze.Name " - + "ORDER BY PublishFreeze.CreateTime ASC" - ) - self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), - [['602', "BXDPublish", "Mouse Phenome Database"]]) - - db_mock.db.execute.return_value.fetchall.return_value = () - db_mock.db.execute.return_value.fetchone.return_value = ( - "BXDPublish", "Mouse Phenome Database" - ) - self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), - [["None", "BXDPublish", "Mouse Phenome Database"]]) - - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + (602, "BXDPublish", "BXD Published Phenotypes"), + ) + self.assertEqual(build_datasets("Mouse", "BXD", + "Phenotypes", db_mock), + [['602', "BXDPublish", + "BXD Published Phenotypes"]]) + cursor.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " + + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " + + "InbredSet WHERE InbredSet.Name = 'BXD' AND " + + "PublishFreeze.InbredSetId = InbredSet.Id AND " + + "InfoFiles.InfoPageName = PublishFreeze.Name " + + "ORDER BY PublishFreeze.CreateTime ASC" + ) + self.assertEqual(build_datasets("Mouse", "MDP", + "Phenotypes", db_mock), + [['602', "BXDPublish", + "Mouse Phenome Database"]]) + + cursor.fetchall.return_value = () + cursor.fetchone.return_value = ( + "BXDPublish", "Mouse Phenome Database" + ) + self.assertEqual(build_datasets("Mouse", "MDP", + "Phenotypes", db_mock), + [["None", "BXDPublish", + "Mouse Phenome Database"]]) + + def test_build_datasets_with_type_phenotypes_and_no_results(self): """Test that correct dataset is returned for a phenotype type with no results """ - db_mock.db.execute.return_value.fetchall.return_value = None - db_mock.db.execute.return_value.fetchone.return_value = (121, - "text value") - self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), - [["None", "121", "text value"]]) - db_mock.db.execute.assert_called_with( - "SELECT PublishFreeze.Name, PublishFreeze.FullName " - "FROM PublishFreeze, InbredSet " - "WHERE InbredSet.Name = 'BXD' AND " - "PublishFreeze.InbredSetId = InbredSet.Id " - "ORDER BY PublishFreeze.CreateTime ASC" - ) - - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_genotypes(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = None + cursor.fetchone.return_value = (121, + "text value") + self.assertEqual(build_datasets("Mouse", "BXD", + "Phenotypes", db_mock), + [["None", "121", + "text value"]]) + cursor.execute.assert_called_with( + "SELECT PublishFreeze.Name, PublishFreeze.FullName " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = 'BXD' AND " + "PublishFreeze.InbredSetId = InbredSet.Id " + "ORDER BY PublishFreeze.CreateTime ASC" + ) + + def test_build_datasets_with_type_genotypes(self): """Test that correct dataset is returned for a phenotype type""" - db_mock.db.execute.return_value.fetchone.return_value = ( - 635, "HLCPublish", "HLC Published Genotypes" - ) - - self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), - [["635", "HLCGeno", "HLC Genotypes"]]) - db_mock.db.execute.assert_called_with( - "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, " - "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND " - "GenoFreeze.InbredSetId = InbredSet.Id AND " - "InfoFiles.InfoPageName = GenoFreeze.ShortName " - + "ORDER BY GenoFreeze.CreateTime DESC" - ) - db_mock.db.execute.return_value.fetchone.return_value = () - self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), - [["None", "HLCGeno", "HLC Genotypes"]]) - - @mock.patch('wqflask.api.gen_menu.g') - def test_build_datasets_with_type_mrna(self, db_mock): + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = ( + 635, "HLCPublish", "HLC Published Genotypes" + ) + self.assertEqual(build_datasets("Mouse", "HLC", + "Genotypes", db_mock), + [["635", "HLCGeno", "HLC Genotypes"]]) + cursor.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, " + "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND " + "GenoFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + "ORDER BY GenoFreeze.CreateTime DESC" + ) + cursor.fetchone.return_value = () + self.assertEqual(build_datasets("Mouse", "HLC", + "Genotypes", db_mock), + [["None", "HLCGeno", "HLC Genotypes"]]) + + def test_build_datasets_with_type_mrna(self): """Test that correct dataset is returned for a mRNA expression/ Probeset""" - db_mock.db.execute.return_value.fetchall.return_value = ( - (112, "HC_M2_0606_P", - "Hippocampus Consortium M430v2 (Jun06) PDNN"), ) - self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[ - "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN" - ]]) - db_mock.db.execute.assert_called_once_with( - "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " - + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " - + "ProbeFreeze, InbredSet, Tissue, Species WHERE " - + "Species.Name = 'Mouse' AND Species.Id = " - + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " - + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " - + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " - + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " - + "ProbeSetFreeze.public > 0 " - + "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC") + db_mock = mock.MagicMock() + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + (112, "HC_M2_0606_P", + "Hippocampus Consortium M430v2 (Jun06) PDNN"), ) + self.assertEqual(build_datasets("Mouse", + "HLC", "mRNA", db_mock), + [["112", 'HC_M2_0606_P', + "Hippocampus Consortium M430v2 (Jun06) PDNN" + ]]) + cursor.execute.assert_called_once_with( + "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " + "ProbeFreeze, InbredSet, Tissue, Species WHERE " + "Species.Name = 'Mouse' AND Species.Id = " + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " + "ProbeSetFreeze.public > 0 " + "ORDER BY -ProbeSetFreeze.OrderList DESC, " + "ProbeSetFreeze.CreateTime DESC") @mock.patch('wqflask.api.gen_menu.build_datasets') - @mock.patch('wqflask.api.gen_menu.g') - def test_build_types(self, db_mock, datasets_mock): + def test_build_types(self, datasets_mock): """Test that correct tissue metadata is returned""" + db_mock = mock.MagicMock() datasets_mock.return_value = [ ["112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"] ] - db_mock.db.execute.return_value.fetchall.return_value = ( - ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue') - ) - self.assertEqual(build_types('mouse', 'random group'), - [['M', 'M', 'Molecular Traits'], - ['H', 'H', 'Molecular Traits'], - ['R', 'R', 'Molecular Traits']]) - db_mock.db.execute.assert_called_once_with( - "SELECT DISTINCT Tissue.Name " - + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " - + "Tissue, Species WHERE Species.Name = 'mouse' " - + "AND Species.Id = InbredSet.SpeciesId AND " - + "InbredSet.Name = 'random group' AND " - + "ProbeFreeze.TissueId = Tissue.Id AND " - + "ProbeFreeze.InbredSetId = InbredSet.Id AND " - + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " - + "ORDER BY Tissue.Name" - ) + with db_mock.cursor() as cursor: + cursor.fetchall.return_value = ( + ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue') + ) + self.assertEqual(build_types('mouse', 'random group', db_mock), + [['M', 'M', 'Molecular Traits'], + ['H', 'H', 'Molecular Traits'], + ['R', 'R', 'Molecular Traits']]) + cursor.execute.assert_called_once_with( + "SELECT DISTINCT Tissue.Name " + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " + "Tissue, Species WHERE Species.Name = 'mouse' " + "AND Species.Id = InbredSet.SpeciesId AND " + "InbredSet.Name = 'random group' AND " + "ProbeFreeze.TissueId = Tissue.Id AND " + "ProbeFreeze.InbredSetId = InbredSet.Id AND " + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " + "ORDER BY Tissue.Name" + ) @mock.patch('wqflask.api.gen_menu.build_types') @mock.patch('wqflask.api.gen_menu.genotypes_exist') @@ -297,7 +321,9 @@ class TestGenMenu(unittest.TestCase): build_types_mock.return_value = [ ['M', 'M', 'Molecular Trait Datasets'] ] - self.assertEqual(get_types(self.test_group), expected_result) + self.assertEqual(get_types(self.test_group, + mock.MagicMock()), + expected_result) @mock.patch('wqflask.api.gen_menu.build_types') @mock.patch('wqflask.api.gen_menu.genotypes_exist') @@ -315,10 +341,8 @@ class TestGenMenu(unittest.TestCase): genotypes_exist_mock.return_value = False build_types_mock.return_value = [] - self.assertEqual(get_types(self.test_group), { - 'mouse': {}, - 'human': {} - }) + self.assertEqual(get_types(self.test_group, mock.MagicMock()), + {'mouse': {}, 'human': {}}) @mock.patch('wqflask.api.gen_menu.build_types') @mock.patch('wqflask.api.gen_menu.genotypes_exist') @@ -345,7 +369,7 @@ class TestGenMenu(unittest.TestCase): 'human': { 'HLC': [['M', 'M', 'Molecular Trait Datasets']], 'BXD': [['M', 'M', 'Molecular Trait Datasets']]}} - self.assertEqual(get_types(self.test_group), + self.assertEqual(get_types(self.test_group, mock.MagicMock()), expected_result) @mock.patch('wqflask.api.gen_menu.build_datasets') @@ -367,7 +391,7 @@ class TestGenMenu(unittest.TestCase): 'BXD': {'Genotypes': 'Test', 'M': 'Test', 'Phenotypes': 'Test'}}} - self.assertEqual(get_datasets(self.test_type), + self.assertEqual(get_datasets(self.test_type, mock.MagicMock()), expected_result) @mock.patch('wqflask.api.gen_menu.build_datasets') @@ -381,7 +405,7 @@ class TestGenMenu(unittest.TestCase): 'H_T1': {}}, 'human': {'HLC': {}, 'BXD': {}}} - self.assertEqual(get_datasets(self.test_type), + self.assertEqual(get_datasets(self.test_type, mock.MagicMock()), expected_result) @mock.patch('wqflask.api.gen_menu.get_datasets') @@ -411,4 +435,4 @@ class TestGenMenu(unittest.TestCase): 'groups': ['groupA', 'groupB', 'groupC', 'groupD'], 'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']} - self.assertEqual(gen_dropdown_json(), expected_result) + self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result) |